I actually prefer option 2 and I have built my router and my plasma cutter like that. I just think it reduces the center of gravity of the whole mass and I have mine about 3:1 ratio and it works a treat. The cable chain I have with all the cables and wires in it runs over the top much better.
If you have a quick look at the router pics on YouTube you will get what I mean.
http://www.youtube.com/watch?v=qLUFL9c9AoQ
Go to 2:32 for the still shot of the Z axis

I opted to go with the linear rails on rectangular section on the X axis instead of the round bar ones as there was too much flex and I changed out the 2 start 5/8 acme screw on the X axis with a 12 start 3/4" anti-backlash one and now it is so much faster and cuts a whole lot quicker.
Stepper motors work better at slow speeds and have more torque so the 12 start thread is much better
I should take some more pictures of it one day and make a short video too.

Rich.